[gmx-users] gmx trjorder help

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Wed Sep 18 14:59:30 CEST 2019


I used gmx trjorder to order my ligand molecules based on the distance from the COM of my protein using the command below:

gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -o ordered.gro -nshell nshell1.xvg -b 20000 -e 20000 -na 10 -r 0.5

I viewed the nshell1.xvg file to see how many ligand molecules were found within the shell at a particular time. I know in the gromacs manual it says "When an index group of the first n waters is made, the ordered trajectory can be used with any GROMACS program to analyze the n closest waters". I presume that I can use this for my ligand molecules too.

The problem I have with this is the "ordered" trajectory file contains all the ligand molecules even the ones not within the cut-off. Can anybody help with this?


More information about the gromacs.org_gmx-users mailing list